Deconvolution may be required to remove out-of-focus information from the images in the stack. Essentially, deconvolution is an algorithm for calculation that places extended signals in the z direction to their correct xy-xz location in the image stack. A variety of programs are available that allow the user to carryout this mathematical process including, AutoDeblur (AutoQuant), HazeBuster/Microtome (Vaytek), Huygens (SVI), AmiraDECONV (TGS), TILLvislON deconvolution (TILL Photonics), 3-d deconvolution (Zeiss). The 3D rendering may be carried out using ray tracing or surface contour based programs such as Huygens (SVI). An example of application of deconvolution to images of bacteria and biofilm associated with sponges is presented with color illustration in Manz et al.69

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